allow dataflow from standaloneJob

modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisAdaptor.pm

@@ -25,6 +25,8 @@ use strict;
 
 use base ('Bio::EnsEMBL::DBSQL::AnalysisAdaptor');
 
+use Bio::EnsEMBL::Hive::URLFactory;
+
 
 =head2 fetch_by_logic_name_or_url
 
@@ -33,11 +35,11 @@ use base ('Bio::EnsEMBL::DBSQL::AnalysisAdaptor');
 =cut
 
 sub fetch_by_logic_name_or_url {
-    my $self                = shift @_;
+    my $self                = shift @_; # can either be $self or class name
     my $logic_name_or_url   = shift @_;
 
     if($logic_name_or_url =~ m{^\w*://}) {
-        return Bio::EnsEMBL::Hive::URLFactory->fetch($logic_name_or_url, $self->db);
+        return Bio::EnsEMBL::Hive::URLFactory->fetch($logic_name_or_url, ref($self) && $self->db);
     } else {
         return $self->fetch_by_logic_name($logic_name_or_url);
     }

modules/Bio/EnsEMBL/Hive/DataflowRule.pm

@@ -51,6 +51,7 @@ package Bio::EnsEMBL::Hive::DataflowRule;
 use strict;
 use Bio::EnsEMBL::Utils::Argument;  # import 'rearrange()'
 use Bio::EnsEMBL::Utils::Exception;
+use Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor;
 
 =head2 new
 
@@ -239,9 +240,9 @@ sub to_analysis {
     #if the 'from' and 'to' share the same adaptor, then use a simple logic_name
     #for the URL rather than a full network distributed URL
 
-    my $ref_rule_adaptor = $self->from_analysis->adaptor;
+    my $ref_rule_adaptor = $self->from_analysis && $self->from_analysis->adaptor;
 
-    if($analysis_or_nt->can('logic_name') and $self->from_analysis and ($ref_rule_adaptor == $analysis_or_nt->adaptor)) {
+    if($analysis_or_nt->can('logic_name') and $ref_rule_adaptor and ($ref_rule_adaptor == $analysis_or_nt->adaptor)) {
       $self->{'_to_analysis_url'} = $analysis_or_nt->logic_name;
     } else {
       $self->{'_to_analysis_url'} = $analysis_or_nt->url($ref_rule_adaptor->db);
@@ -250,8 +251,12 @@ sub to_analysis {
   # lazy load the analysis object if I can
   if(!defined($self->{'_to_analysis'}) and defined($self->to_analysis_url)) {
 
-    $self->{'_to_analysis'} = $self->adaptor->db->get_AnalysisAdaptor->fetch_by_logic_name_or_url($self->to_analysis_url)
-        or die "Cannot fetch analysis from logic_name or url '".$self->to_analysis_url."' for dataflow rule with id='".$self->dbID."'\n";
+    my $url = $self->to_analysis_url;
+
+    $self->{'_to_analysis'} = $self->adaptor
+        ?  $self->adaptor->db->get_AnalysisAdaptor->fetch_by_logic_name_or_url($url)
+        :  Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor->fetch_by_logic_name_or_url($url)
+    or die "Cannot fetch analysis from logic_name or url '$url' for dataflow rule with id='".$self->dbID."'\n";
 
   }
   return $self->{'_to_analysis'};

scripts/standaloneJob.pl

@@ -6,9 +6,11 @@ use Getopt::Long qw(:config pass_through);
 use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::Hive::Process;
 use Bio::EnsEMBL::Hive::AnalysisJob;
-use Bio::EnsEMBL::Hive::Utils ('script_usage', 'load_file_or_module', 'parse_cmdline_options', 'stringify');
+use Bio::EnsEMBL::Hive::Utils ('script_usage', 'load_file_or_module', 'parse_cmdline_options', 'stringify', 'destringify');
 
-my ($reg_conf, $help, $debug, $no_write);
+use Data::Dumper;
+
+my ($reg_conf, $help, $debug, $no_write, $flow_into);
 
 my $module_or_file = shift @ARGV or script_usage();
 
@@ -17,6 +19,7 @@ GetOptions(
            'debug=i'            => \$debug,
            'reg_conf|regfile=s' => \$reg_conf,
            'no_write|nowrite'   => \$no_write,
+           'flow_into|flow=s'   => \$flow_into,
 );
 
 if ($help or !$module_or_file) {
@@ -33,7 +36,18 @@ my $process = $runnable_module->new();
 my $job = Bio::EnsEMBL::Hive::AnalysisJob->new();
 my ($param_hash, $param_list) = parse_cmdline_options();
 $job->param_init( 1, $process->param_defaults(), $param_hash );
-$job->dataflow_rules( 1, [] );  # dataflow switched off by default
+
+$flow_into = $flow_into ? destringify($flow_into) : []; # empty dataflow for branch 1 by default
+$flow_into = { 1 => $flow_into } unless(ref($flow_into) eq 'HASH'); # force non-hash into a hash
+foreach my $branch_code (keys %$flow_into) {
+    my $heirs = $flow_into->{$branch_code};
+
+    $heirs = [ $heirs ] unless(ref($heirs)); # force scalar into an arrayref first
+
+    my @dataflow_rules = map { Bio::EnsEMBL::Hive::DataflowRule->new( -to_analysis_url => $_ ) } @$heirs;
+
+    $job->dataflow_rules( $branch_code, \@dataflow_rules );
+}
 
 my $input_id = stringify($param_hash);
 $job->input_id( $input_id );
@@ -71,8 +85,9 @@ __DATA__
 
     standaloneJob.pl is an eHive component script that
         1. takes in a RunnableDB module,
-        2. creates a standalone job outside an eHive database by initializing parameters from command line arguments
+        2. creates a standalone job outside an eHive database by initializing parameters from command line arguments (ARRAY- and HASH- arguments can be passed+parsed too!)
         3. and runs that job outside the database.
+        4. can optionally dataflow into tables fully defined by URLs
     Naturally, only certain RunnableDB modules can be run using this script, and some database-related functionality will be lost.
 
 =head1 USAGE EXAMPLES
@@ -93,12 +108,17 @@ __DATA__
         # Run a job with given parameters, but skip the write_output() step:
     standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::FailureTest -no_write -time_RUN=2 -time_WRITE_OUTPUT=3 -state=WRITE_OUTPUT -value=2
 
+        # Run a job and re-direct its dataflow into tables:
+    standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::JobFactory -inputfile foo.txt -delimiter '\t' -column_names "[ 'name', 'age' ]" 
+                        -flow_into "{ 2 => ['mysql://ensadmin:ensembl@127.0.0.1:2914/lg4_triggers/foo', 'mysql://ensadmin:ensembl@127.0.0.1:2914/lg4_triggers/bar'] }"
+
 =head1 SCRIPT-SPECIFIC OPTIONS
 
     -help               : print this help
     -debug <level>      : turn on debug messages at <level>
     -no_write           : skip the execution of write_output() step this time
     -reg_conf <path>    : load registry entries from the given file (these entries may be needed by the RunnableDB itself)
+    -flow_out "<hash>"  : defines the dataflow re-direction rules in a format similar to PipeConfig's - see the last example
 
     NB: all other options will be passed to the runnable (leading dashes removed) and will constitute the parameters for the job.